Search

The coupling between nitrification and N2 gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N2 gas. Here we show, in oxic riverbeds, that the pattern of N2 gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N2 gas that 20 years’ research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle., The N cycle involves complex, microbially-mediated shuttling between ammonium, nitrite and nitrate, with climatically important greenhouse gas byproducts. Here the authors use isotope labeling experiments in river sediments and find a cryptic new step in the N cycle between nitrification and the removal of fixed N through N2 gas production.

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%-42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.

Net emissions of the potent GHG methane from ecosystems represent the balance between microbial methane production (methanogenesis) and oxidation (methanotrophy), each with different sensitivities to temperature. How this balance will be altered by long-term global warming, especially in freshwaters that are major methane sources, remains unknown. Here we show that the experimental warming of artificial ponds over 11 years drives a disproportionate increase in methanogenesis over methanotrophy that increases the warming potential of the gases they emit. The increased methane emissions far exceed temperature-based predictions, driven by shifts in the methanogen community under warming, while the methanotroph community was conserved. Our experimentally induced increase in methane emissions from artificial ponds is, in part, reflected globally as a disproportionate increase in the capacity of naturally warmer ecosystems to emit more methane. Our findings indicate that as Earth warms, natural ecosystems will emit disproportionately more methane in a positive feedback warming loop.\ud \ud

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO2 g−1 (dry sediment) d−1, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 105 to 1.5 × 107 and 2.1 × 104 to 2.5 × 105 copies g−1 dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.

Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (

Anthropogenic nitrogen fixation and subsequent use of this nitrogen as fertilizer has greatly disturbed the global nitrogen cycle. Rivers are recognized hotspots of nitrogen removal in the landscape as interaction between surface water and sediments creates heterogeneous redox environments conducive for nitrogen transformations. Our understanding of riverbed nitrogen dynamics to date comes mainly from shallow sediments or hyporheic exchange flow pathways with comparatively little attention paid to groundwater-fed, gaining reaches. We have used 15N techniques to quantify in situ rates of nitrate removal to 1m depth within a groundwater-fed riverbed where subsurface hydrology ranged from strong upwelling to predominantly horizontal water fluxes. We combine these rates with detailed hydrologic measurements to investigate the interplay between biogeochemical activity and water transport in controlling nitrogen attenuation along upwelling flow pathways. Nitrate attenuation occurred via denitrification rather than dissimilatory nitrate reduction to ammonium or anammox (range = 12 to >17000 nmol 15N L-1 h-1). Overall, nitrate removal within the upwelling groundwater was controlled by water flux rather than reaction rate (i.e. Damkohler numbers 80% of nitrate removal occurs within sediments not exposed to hyporheic exchange flows under baseflow conditions, illustrating the importance of deep sediments as nitrate sinks in upwelling systems.

Anthropogenic nitrogen pollution is a critical problem in freshwaters. Although riverbeds are known to attenuate nitrate, it is not known if large woody debris (LWD) can increase this ecosystem service through enhanced hyporheic exchange and streambed residence time. Over a year, we monitored the surface water and pore water chemistry at 200 points along a ~ 50 m reach of a lowland sandy stream with three natural LWD structures. We directly injected 15N-nitrate at 108 locations within the top 1.5 m of the streambed to quantify in situ denitrification, anammox and dissimilatory nitrate reduction to ammonia, which, on average, contributed 85, 10 and 5% of total nitrate reduction, respectively. Total nitrate reducing activity ranged from 0 to 16 µM h−1 and was highest in the top 30 cm of the stream bed. Depth, ambient nitrate and water residence time explained 44% of the observed variation in nitrate reduction; fastest rates were associated with slow flow and shallow depths. In autumn, when the river was in spate, nitrate reduction (in situ and laboratory measures) was enhanced around the LWD compared with non-woody areas, but this was not seen in the spring and summer. Overall, there was no significant effect of LWD on nitrate reduction rates in surrounding streambed sediments, but higher pore water nitrate concentrations and shorter residence times, close to LWD, indicated enhanced delivery of surface water into the streambed under high flow. When hyporheic exchange is too strong, overall nitrate reduction is inhibited due to short flow-paths and associated high oxygen concentrations.

SUMMARY 1. Many rivers are oversaturated in methane (CH4) and carbon dioxide (CO2) relative to the atmosphere, but we know little about the biological controls on the balance between these two important greenhouse gases and how they might respond to warming. 2. We characterise the potential response to temperature in the biological production of CO2 and CH4 and the subsequent microbial oxidation of that CH4, that is the sink and source components of the CH4 cycle, in contrasting river bed sediments: fine sediments, which are largely anoxic, and oxic, coarse gravels. 3. In the fine sediments, anaerobic production of both CH4 and CO2 increased with temperature, with apparent activation energies for each being 0.51 eV and 0.24 eV, respectively. The difference between the two resulted in a 4% increase in the ratio of CH4:CO2 production for a 1 °C increase in temperature. 4. In the coarse gravels, microbial CH4 oxidation showed no response to temperature at CH4 concentrations characteristic of these gravel beds (30–200 nmol CH4 L 1 ), due to strong substrate limitation. In contrast, at higher (although still rate limiting) CH4 concentrations, more characteristic of the fine sediment patches (2–4 lmol CH4 L 1 ), CH4 oxidation exhibited an increasingly strong response to temperature, eventually exceeding that for CH4 production. 5. In the fine sediment, the surface layers had a CH4 oxidation capacity over 100 times greater than the gravels and the kinetic response to differing pore water CH4 concentrations meant CH4 was oxidised some 2000 times faster in the fine sediment patches compared with the coarse gravels. 6. The calculated kinetic and temperature responses showed that with warming, methanogenesis is unlikely to outstrip methanotrophy and the ratio of CO2 to CH4 emitted could be conserved. Consequently, any changes in the efflux ratio of CH4 to CO2 are unlikely to be due to the incapacity of methanotrophy to respond to CH4 production, but rather to a physical bypassing of the methanotrophic community (e.g. through ebullition or transport via plant stems) or contraction of the oxic layer.

Environmental anaerobic ammonium oxidation (anammox) was demonstrated for the first time in 2002, using 15 N labeling, in homogenized sediment from the Skagerrak, where it accounted for up to 67% of N 2 production. We returned to some of these original sites in 2010 to make measurements of nitrogen and carbon cycling under conditions more representative of those in situ , quantifying anammox and denitrification, together with oxygen penetration and consumption, in intact sediment cores. Overall, oxygen consumption and N 2 production decayed with water depth, as expected, but the drop in N 2 production was relatively more pronounced. Whereas we confirmed the dominance of N 2 production by anammox (72% and 77%) at the two deepest sites (∼700 m of water), anammox was conspicuously absent from two shallower sites (∼200 m and 400 m). At the shallower sites, we could measure no anammox activity with either intact or homogeneous sediment, and quantitative PCR (16S rRNA) gave a negligible abundance of anammox bacteria in the anoxic layers. Such an absence of anammox, especially at one locale where it was originally demonstrated, is hard to reconcile. Despite the dominance of anammox at the deepest sites, anammox activity could not make up for the drop in denitrification, and assuming Redfield ratios for the organic matter being mineralized, the estimated retention of fixed N actually increased to 90% to 97% of that mineralized, whereas it was 80% to 86% at the shallower sites.

Emergent vegetation in river beds can play a significant role in nutrient cycling in riverine sediments. We analysed and compared pore water NO3 − concentration gradients in the sediments of the River Leith, Cumbria, UK, in the presence and absence of emergent vegetation (dominated by Sparganium spp.). High resolution (1 cm interval), in situ, vertical profiles of NO3 − to 30 cm depth were measured using deployment of diffusive equilibrium in thin films probes on four occasions from July to September 2010. We found significantly (p

Water pathways through permeable riverbeds are multi-dimensional, including lateral hyporheic exchange flows as well as vertical (upwelling and downwelling) fluxes. The influence of different pathways of water on solute patterns and the supply of nitrate and other redox-sensitive chemical species in the riverbed is poorly understood but could be environmentally significant. For example, nitrate-rich upwelling water in the gaining reaches of groundwater-fed rivers has the potential to supply significant quantities of nitrate through the riverbed to surface waters, constraining opportunities to deliver the goals of the EU Water Framework Directive to achieve ‘good ecological status’. We show that patterns in porewater chemistry in the armoured river bed of a gaining reach (River Leith, Cumbria) reflect the spatial variability in different sources of water; oxic conditions being associated with preferential discharge from groundwater and reducing conditions with longitudinal and lateral fluxes of water due to water movement from riparian zones and/or hyporheic exchange flows. Our findings demonstrate the important control of both vertical and lateral water fluxes on patterns of redox-sensitive chemical species in the river bed. Furthermore, under stable, baseflow conditions (

Laboratory incubations with river-bed sediment collected from riffles and pools were used to quantify potential pathways of dissimilatory nitrate reduction in the hyporheic zone of a groundwater-fed river. Sediments collected from between 5-cm and 86-cm depth in the bed of the River Leith, Cumbria, United Kingdom, were incubated with a suite of 15N-labeled substrates (15NO { , 15NH z , and 14NO { ) to quantify nitrate reduction via denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox). Denitrification was the dominant pathway of dissimilatory nitrate reduction in the hyporheic sediments, although recovery of 15N from the ammonium pool indicated that DNRA was also active. The potential for anammox was confirmed by the production of 29N2 during the 15NH z and 14NO { incubation, but it was much smaller than denitrification. Potential rates of denitrification were highest in shallow sediments and decayed exponentially with depth thereafter. There were clear differences in denitrification activity between riffle and pool sediments. After the production of 15N-N2 had stabilized, we added a spike of bacteriological peptone to determine the effect of complex organic substrates on denitrification potential. The potential rate of denitrification increased uniformly at all sediment depths but the total amount of denitrification fueled by the organic substrates decreased markedly with depth, from 90% in the shallow sediments to 30% in the deepest sediments. In addition, a considerable fraction of the 15 NO { could not be accounted for, which suggested that up to 87% of it had been assimilated in the deepest sediments. The hyporheic zone is a key area of biogeochemical activity between the surface water and groundwater of streams and rivers (Boulton et al. 2010). Here exchanges of dissolved and particulate organic matter, oxygen, and nutrients drive the cycling of the key biotic macronutrients (C, H, N, P, S), in turn, sustaining the productivity of the sediment strata in this ‘dynamic ecotone’ at or beneath the river bed (Gilbert et al. 1990). The contribution that biogeochemical activity within the hyporheic zone makes to the river as a whole is, in turn, governed by the balance between surface and subsurface flow and the intensity of subsurface processes (Findlay 1995). One particular biogeochemical process that has received a great deal of attention is denitrification: the biological

Variations in the overall and depth-specific significance of anammox were measured using (15) N isotope experiments in both bioirrigated and undisturbed sediments of the Medway Estuary, UK. This was performed over two surveys, alongside FISH experiments, to identify and track shifts in the relative abundance of anammox organisms with depth. In Survey 1 (initially screening for the presence of anammox), the potential for anammox (ra) decreased from 32% upstream to 6% downstream. In Survey 2, depth-specific values of ra varied between a maximum of 37% upstream and a minimum of 4% downstream. This was linked to a small population of anammox organisms accounting for 1-8% of total bacteria with depth in Survey 1 and 1-3% in Survey 2. The relationship between the relative abundance of anammox cells and the potential contribution of anammox to total N(2) production did not however correlate. In Survey 2, infaunal disruption of the sediment substrata, and concomitant fluctuations of O(2) over depth, did not appear to inhibit the potential for anammox, even at the most bioturbated site. Moreover, deficits detected in the retrieval of (15) N gas from denitrification in Survey 2 may imply potential links between dissimilatory nitrate reduction to ammonium and anammox in estuarine sediments.

We measured denitrification, anaerobic ammonium oxidation (anammox), oxygen uptake, nutrient exchange, and pore-water profiles of oxygen in intact sediments at three sites in the southern North Sea, which we experimentally exposed to different oxygen saturations (ambient and , 33% of air-saturation for oxygen [i.e., our hypoxic treatment]) over 14 months. Denitrification ranged from 1 mmol N m22 h21 to 21 mmol N m22 h21, anammox 0.2 mmol N m22 h21 to 5.7 mmol N m22 h21, and oxygen uptake 47 mmol O2 m22 h21 to 631 mmol O2 m22 h21. The seasonal patterns under ambient oxygen were correlated with those in the hypoxic treatment; though, on the whole, the magnitude of flux was different. On average, under hypoxia, both the penetration and consumption of oxygen decreased by , 50%, denitrification increased by 32%, and anammox remained constant. Anammox accounted for between 10% and 20% of the total N2 production, which agrees with expectations for waters of these depths (30–80 m). Under ambient oxygen the sediments were strong sources of nitrate to the overlying water, 12 mmol NO { m22 h21 on average, but under hypoxia total N mineralization decreased by 46% and nitrate exchanged ceased. Short-term hypoxia alters the balance between available N returned to the overlying water, primarily as NO { , and that removed from the ecosystem as N2 gas. The coastal margins and continental shelves comprise , 9% of the total area of ocean sediments, but are responsible

Methane (CH(4)) and carbon dioxide (CO(2)) are the dominant gaseous end products of the remineralization of organic carbon and also the two largest contributors to the anthropogenic greenhouse effect. We investigated whether warming altered the balance of CH(4) efflux relative to gross primary production (GPP) and ecosystem respiration (ER) in a freshwater mesocosm experiment. Whole ecosystem CH(4) efflux was strongly related to temperature with an apparent activation energy of 0.85 eV. Furthermore, CH(4) efflux increased faster than ER or GPP with temperature, with all three processes having sequentially lower activation energies. Warming of 4 degrees C increased the fraction of GPP effluxing as CH(4) by 20% and the fraction of ER as CH(4) by 9%, in line with the offset in their respective activation energies. Because CH(4) is 21 times more potent as a greenhouse gas, relative to CO(2), these results suggest freshwater ecosystems could drive a previously unknown positive feedback between warming and the carbon cycle.

Organism size is one of the key determinants of community structure, and its relationship with abundance can describe how biomass is partitioned among the biota within an ecosystem. An outdoor freshwater mesocosm experiment was used to determine how warming of � 41C would affect the size, biomass and taxonomic structure of planktonic communities. Warming increased the steepness of the community size spectrum by increasing the prevalence of small organisms, primarily within the phytoplankton assemblage and it also reduced the mean and maximum size of phytoplankton by approximately one order of magnitude. The observed shifts in phytoplankton size structure were reflected in changes in phytoplankton community composition, though zooplankton taxonomic composition was unaffected by warming. Furthermore, warming reduced community biomass and total phytoplankton biomass, although zooplankton biomass was unaffected. This resulted in an increase in the zooplankton to phytoplankton biomass ratio in the warmed mesocosms, which could be explained by faster turnover within the phytoplankton assemblages. Overall, warming shifted the distribution of phytoplankton size towards smaller individuals with rapid turnover and low standing biomass, resulting in a reorganization of the biomass structure of the food webs. These results indicate future environmental warming may have profound effects on the structure and functioning of aquatic communities and ecosystems.

Due to a combination of local methanogenesis and high background concentrations in the groundwater, water in the River Lambourn is 51 times supersaturated with methane (162 nmol CH4 L−1). Pore-water concentrations of methane in the gravels of the riverbed were much lower throughout the year (71 nmol CH4 L−1), suggesting significant methane oxidation. To investigate the potential for methane oxidation as a novel chemosynthetic source of carbon to the food web, we made simultaneous measurements, in laboratory chambers, of primary production, respiration, and methane oxidation associated with the gravels. Biomass-specific net primary production was up to 2.7 µmol O2 mg−1 chlorophyll (Chl) h−1 and was similarly high for respiration (2.7 µmmol O2 mg−1 Chl h−1). We also found active methane (CH4) oxidation with the rate increasing in proportion to concentration. At the maximum rate of 0.18 µmol CH4 mg−1 Chl h−1 and a growth efficiency of 0.8, net carbon fixation via methane oxidation was equivalent to 6% of the carbon fixed via net photosynthetic primary production. However, production via methane oxidation could be proportionately much greater under the shade of the profuse instream or riparian vegetation, deep in the gravels, and especially during winter, when light is limiting (< 25 µmol quanta m−2 s−1).

We investigated the accumulation and biogeochemical cycling of organic matter beneath Ranunculus plants in a lowland river. Organic carbon accumulated beneath the plants at a mean rate of 20 mmol C m ―2 h ―1 . Annual gross primary production for both Ranunculus and its biofilm, and the microphytobenthos, could account for 26% of the carbon accumulated. The remainder was attributable to organic carbon in both suspended particulate matter (77%) and that associated with sands saltating along the bottom (33%). Maximum carbon oxidation occurred in spring and early summer and declined thereafter. The efflux of CO 2 was greater than the carbon equivalents due to reduction of O 2 , NO 3 ― and SO 4 2― measured at the surface, which suggested a significant contribution to carbon oxidation from the subsurface and some oxidation via alternative electron acceptors. The peak in carbon oxidation could not be accounted for by either rising temperature or primary production but tracked the quality of recently deposited allochthonous organic matter. The ratio of carbon oxidation to total organic carbon accumulation suggested that 19% of the organic matter deposited was remineralised on an annual basis, although this reached 58% in June. We calculate that a total of 3·6 mol N m ―2 y ―1 was mineralised in the sediment, of which 11% could be accounted for by the measured efflux of NH 4 + . The remainder could be accounted for by the N demand from primary production (67% macrophytes/biofilm; 36% phytobenthos).

We measured the δ13C values of dominant primary consumers and their potential food sources in a groundwater-fed lowland river. The δ13C of most consumers, such as Gammarus and Simulium, reflected that of the dominant forms of photosynthetic production, whereas the cased larvae of two caddis flies (Agapetus and Silo) were consistently 13C depleted (mean δ13C: -41.2% and -40.4%, respectively) throughout the year. The river water was supersaturated (approximately 50 times atmospheric) with methane, reflecting both supersaturation in the groundwater and local production in fine sediments. We measured appreciable rates of methane oxidation, relative to water only controls, in the biofilms on gravel, on the caddis fly cases, and on the bottom of larger rocks. In addition, there was a marked difference in the ratio of methane-oxidizing potential to chlorophyll across those substrata. This ratio was below detection in the biofilm (i.e., no methane oxidation) on the tops of rocks, greater on the bottom of rocks, and maximal for the gravels and the caddis cases. If the caddis larvae acquire most of their carbon by grazing the tops of such rocks (where they are normally found), then they must acquire their depleted δ13C values by occasionally grazing biofilm where the ratio of methane oxidation to chlorophyll was much greater, and the most likely candidate is from their own or conspecific cases. Grazing methane-oxidizing bacteria could provide the caddis larvae with up to 30% of their carbon, which could represent a true subsidy from an ancient groundwater source.

We assayed sediment for the anammox reaction at 40 sites from 9 estuaries during the summer of 2004. The anammox reaction was detected at all sites with its potential contribution to the production of N 2 (ra, %) ranging from 3 % (> 2 nmol N 2 ml -1 wet sediment for anammox after 24 h), below this, though still detectable, anammox was underestimated with 15 NH 4 + . The decrease in the estimate for anammox with 15 NH 4 + relative to 15 NO 3 - was partly explained by a decrease in the recovery of N 2 gas, probably as a result of significant dissimilatory nitrate reduction to ammonium (DNRA) in some of the slurries. The potential interference from DNRA in the anammox assay, however, would be low, with the probability of anamox making 30 N 2 (A 30 N 2 ) being about 1.4 %. Our findings provide firm evidence that the anammox reaction is widespread in estuarine sediments.

We investigated anaerobic ammonium oxidation (anammox) in continental shelf and slope sediments of the Irish and Celtic Seas by using anammox specific ladderane biomarker lipids. We used the presence of an intact ladderane phospholipid as a direct indicator for living anammox bacteria, and compared it with the abundance of ladderane core lipids derived from both living and dead bacterial biomass. All investigated sediments contained ladderane core lipids as well as the intact ladderane phospholipid, in agreement with 15 N-labeling experiments, which revealed anammox activity at all sites. Ladderane core lipid and intact ladderane phospholipid concentrations were significantly correlated ( R 2 = 0.957 and 0.464, respectively) with anammox activity over the transect of the continental shelf and slope sediments. In the Irish Sea (50–100 m water depth) highest abundances of the intact ladderane phospholipid were found in the upper 2 cm of the sediment, indicating a zone of active anammox. A sharp decline further down-core suggested a strong decrease in anammox biomass and rapid degradation of the intact lipids. In comparison, ladderane core lipids were 1–2 orders of magnitude higher in concentration than the intact ladderane phospholipid and accumulated as dead cell remnants with depth. In the slope sediments of the Celtic Sea both ladderane core lipids and the intact ladderane phospholipid were found in sediments at water depths ranging from 500 to 2000 m. Here, anammox seemed to be active at greater depths of the sediment (>2 cm). Mean abundances of both intact and core ladderane lipids in whole sediment cores increased downslope, indicating an increasing importance of anammox in deeper slope sediments.

Summary 1. The emission of biogenic gases, particularly methane, is usually associated with wetlands rather than clean streams. Here, we investigated methane production from a southern English chalk stream, where increased sedimentation, compounded by extensive macrophyte growth, may have altered ecosystem function. 2. Cover of the channel by the dominant macrophyte, Ranunculus penicillatus, peaked in August, when plant beds were associated with low water velocity and the accumulation of sediment (90%) of the methane flux is transported to the atmosphere through the Ranunculus stems. 5. Although the total flux of methane from U.K. chalk streams is probably relatively modest (estimated at 3.2 × 10−6 Tg CH4 year−1), this phenomenon changes our perception of the health of these ecosystems and indicates another deleterious side effect of agriculture.

Managing diffuse pollution in catchments is a major issue for environmental managers planning to meet water quality standards and comply with the EU Water Framework Directive. A major source of diffuse pollution is from nitrogen, with high nitrate concentrations affecting water supplies and in-stream ecology. A dynamic, process based model of flow, nitrate and ammonium (INCA-N) has been applied to the Hampshire Avon as part of the NERC Macronutrient Cycles Programme to link upstream and downstream measurements of water chemistry. The model has been calibrated and validated against Environment Agency discharge and solute chemistry data, as well as a data set collected from a river site immediately upstream of the estuary tidal limit. Upstream measurements of denitrification at six sites have been used to evaluate nitrate removal rates in vegetated and non-vegetated conditions. Results show that sediments underlying vegetation were associated with significantly higher rates of nitrate removal than un-vegetated sediments (with an average increase of 245%). These data have been used to scale up rates of nitrate loss to the whole catchment scale and have been implemented via the model. The effects of streambed geology and macrophyte cover on catchment-scale nitrogen dynamics are explored and nutrient fluxes entering the estuary are evaluated. The model is used to test a strategy for nitrogen reduction assessed using a nitrate vulnerable zone (NVZ) methodology. It suggests that nitrate and ammonium concentrations could be reduced by 10% in 10 years and much lower nitrogen level can be achieved but only over a long time period.

Anammox, i.e. the anaerobic oxidation of NH4 + with NO2 - to N2, has redefined our understanding of nitrogen cycling in aquatic ecosystems. The isotope pairing technique (IPT) is the dominant tool for quantifying denitrification in intact sediments, but it cannot distinguish anammox from denitrification as sources of N2 and may, where anammox is significant, lead to large errors in the estimate of true N2 production. In a previous study, the IPT was revised in theory and a solution was proposed whereby the parameter r14, i.e. the ratio of 14 NO3 - to 15 NO3 - in the NO3 - reduction zone is used to correct the IPT in the presence of anammox. We begin by exploring the limitations of the 2 indirect techniques previously proposed for estimating r14. The first, based on the contribution of anammox to N2 production (ra) in sediment slurry incubations, underestimates anammox and cannot fully correct the IPT. The second, derived from the production of 15 N-N2 gas as a function of 15 NO3 - concentration, although valid in sieved sediment, was ineffective in natural intact sediments. In con- trast, a newly developed direct technique based on the 15 N-labelling of N2O, corrects the IPT in the presence of significant anammox (48% of N2 formation) in natural sediment and can even distinguish between anammox and denitrification in estuarine sediment with a lower anammox contribution (21%). We contrast these findings with sediments where anammox is minimal (

Seasonal measurements of sedimentary sulfate reduction at a freshwater site (site 1) and a brackish/marine site (site 4) in the upper estuary of the Great Ouse, Norfolk, UK revealed very similar integrated annual rates of sulfate reduction: 5.3 and 3.7 mol sulfate m−2 year−1, respectively, but two distinctly different seasonal cycles. At site 4 sulfate reduction followed a seasonal pattern with summer maxima and winter minima, suggesting temperature dependence, but in contrast at site 1 there was no distinct seasonal cycle. Use of 16S rRNA-targeted oligonucleotide probes to investigate the active sulfate reducing bacterial (SRB) populations suggested that populations of SRB remained relatively constant at site 4 throughout the year. However, at site 1 distinct peaks in signal from a Desulfovibrio spp.-targeted probe were measured which corresponded with peaks in sulfate reduction activity. In addition, sedimentary profiles suggested that both sulfate reduction activity and active SRB populations peaked at 0–5 cm into the sediment at site 1 but deeper into the sediment at 9–10 cm at site 4. The results indicate that SRB population dynamics are more complex than process measurements would suggest.

This chapter provides a synthesis of the broadscale patterns of anammox across a spectrum of aquatic ecosystems and to put forward some hypotheses as to what regulates anammox and the total flux of N in such systems. Research into anammox falls largely into two distinct aquatic ecosystems: (i) its role in the anaerobic oxidation of ammonium in the suboxic layers of aquatic sediments, where the respective reactions and ecophysiologies are compressed into fractions of centimeters; and (ii) the same ecosystem function, but distributed over depths of tens of meters in the oxygen minimum zones (OMZs) of the global ocean. The chapter focuses on the results obtained using slurries of homogenized sediment, and then focuses on the data derived with intact sediment cores, and, finally, draw comparisons between the two at the end, without dwelling too long on the respective complexities of each method. Anammox bacteria appear active in both low-oxygen and suboxic waters, and such conditions are often considered as prerequisites for denitrification, since oxygen represses synthesis and activity of denitrifying enzymes, though the effect may be more subtle.

Alteration of the global nitrogen cycle by man has increased nitrogen loading in waterways considerably, often with harmful consequences for aquatic ecosystems. Dynamic redox conditions within riverbeds support a variety of nitrogen transformations, some of which can attenuate this burden. In reality, however, assessing the importance of processes besides perhaps denitrification is difficult, due to a sparseness of data, especially in situ, where sediment structure and hydrologic pathways are intact. Here we show in situ within a permeable riverbed, through injections of (15)N-labeled substrates, that nitrate can be either consumed through denitrification or produced through nitrification, at a previously unresolved fine (centimeter) scale. Nitrification and denitrification occupy different niches in the riverbed, with denitrification occurring across a broad chemical gradient while nitrification is restricted to more oxic sediments. The narrow niche width for nitrification is in effect a break point, with the switch from activity "on" to activity "off" regulated by interactions between subsurface chemistry and hydrology. Although maxima for denitrification and nitrification occur at opposing ends of a chemical gradient, high potentials for both nitrate production and consumption can overlap when groundwater upwelling is strong.

A diagenetic model is presented which considers nitrate reduction by both denitrification and Dissimilatory Nitrate Reduction to Ammonium (DNRA). This work builds on an existing model (Kelly-Gerreyn et al 1999; Mar Ecol Prog Ser 177:37-50). Previous models have assumed nitrate reduction to be solely due to denitrification. This paper questions the reliability of this assumption in coastal areas and suggests that DNRA can account for a high proportion of nitrate reduction. Data from a North Sea estuary (the lower Gt. Ouse, Norfolk, UK) containing high nutrient concentrations (mean 406 μM NO 3 - ) are used to derive a relationship between temperature and the proportioning of nitrate reduction driven by nitrate from the overlying water into denitrification and DNRA. The relationship is assumed to apply to total nitrate reduction. The result is a function which shows that DNRA and denitrification occur at all temperatures but that DNRA is the favoured pathway at the extremes of the observed temperatures ( 17°C) while denitrification is favoured only in a narrow range of temperatures (14 to 17°C). The mechanism is probably an adaptive response of different nitrate-reducing bacteria to temperature. This temperature relationship is implemented in the model and used to successfully simulate both observed rates of uncoupled denitrification (4 to 228 μmolN m -2 h -1 ), denitrification fuelled by nitrate in the overlying water (D w ), and calculated rates of DNRA fuelled by nitrate in the overlying water (DNRA w ) (measured nitrate flux - measured D w rate). In contrast, standard diagenetic formulae for nitrate reduction (i.e. by denitrification only) cannot satisfactorily reproduce the D w rates observed in these sediments. It is concluded that temperature is an important controlling factor for partitioning nitrate reduction into DNRA and denitrification in the lower Gt. Ouse sediments. This temperature effect implies that during an extended warm summer in temperate estuaries receiving high nitrate inputs, nitrate reduction may contribute to, rather than counteract, a eutrophication event. Diagenetic models of the nitrogen cycle in coastal areas should include DNRA.

The geomorphology of the present day and Holocene (3000 years ago) Humber estuary, United Kingdom, are described. More than 90% of the intertidal area and sediment accumulation capacity of the estuary has been lost to reclamation over this period. A similar situation prevails in many other urbanized estuaries. Nutrient budgets for the modern estuary are presented demonstrating little trapping of nutrients, due to the loss of intertidal areas. A speculative budget for the Humber during the Holocene is constructed, which suggests that the estuary was then an efficient sink for nitrogen and phosphorus. A budget is presented describing how nutrient cycling might operate in the Humber with contemporary nutrient loadings, but with the pre-reclamation geography. This suggests that in this form the estuary would significantly attenuate nutrient fluxes to the North Sea. The results are discussed in terms of options for managed realignment of estuaries in response to predicted sea-level rise.

Seasonal measurements of organic matter mineralisation by oxygen uptake and denitrification were carried out from July 1996 to March 1998 along a -200 km transect of the River Thames estuary, UK. There was a distinct gradient of decreasing rates of organic matter mineralisation seaward, which was related to the concentration of suspended solids and sedimentary organic carbon (C) at each site. There was clear seasonality and highest rates of oxygen uptake (10 056 pmol O 2 m -2 h -1 ) at the muddy sites, but lower rates and non-temperature-dependent oxygen uptake at the sandier sites. Denitrification, both that driven by nitrate from the overlying water (D w ) and that coupled to nitrification in the sediment (D n ), followed a similar trend to oxygen uptake, from negligible rates of approximately 1 pmol N m -2 h -1 for both D w and D n at the furthest offshore site, Site 12, to 11 407 and 8209 pmol N m -2 h -1 , respectively, at the inner muddy Site 1. The Thames estuary is heterotrophic and a very efficient organic C filter, trapping and remineralising 77% of its organic C-input. Attenuation of fluvial nitrate loads was regulated by freshwater flow. Minimal attenuation (3 %) occurred during peak flows (i.e. during periods of shortest freshwater flushing time) and > 100 % attenuation during periods of lowest freshwater flow (longest flushing times). Including the sewage treatment works (STWs) nitrate load in this calculation reduced the degree of attenuation of the nitrate load to, on average, 11%. Annual rates of D w and D n for an inner area of 125 km 2 were 112 and 85 Mmol N yr -1 , respectively, with a total rate of 196 Mmol N yr -1 (2744 t), which was equivalent to 9% of the total dissolved inorganic nitrogen (DIN) load for 1995-96. A mean denitrification rate (D w ) of 0.64 mol N m -2 yr -1 , based on measurements in 4 east coast estuaries, was used to estimate a total rate of denitrification for the entire area of UK east coast estuaries. The total rate of 0.81 Gmol N yr -1 represented 16% attenuation of the total fluvial discharge of nitrate (-6 Gmol N yr -1 ) to the UK's east coast estuaries (1995-96) and hence a 16% reduction in the UK nitrate load to the North Sea.

The fate of nitrogen (N) in the bottom sediments of the upper Great Ouse estuary, England, was examined over the course of a year. The sedirnents were consistent sinks for NO3from the overlying river water, and were weak sources of NH,'. Simultaneous measurements of oxygen uptake, nutrient exchange and sulphate reduction, when combined with the measured C:N ratios of the sediment organic matter, permitted calculation of the amount of N released within the sediment by organic matter mineralisation. With the exception of a site w ~ t h thixotropic sediment, at all other sites the amount of inorganic N entering the sedlment by transport from the overlying water and by internal ammonification of organic matter was not matched by measured exports of N from the sedirnents. We calculate that >90% of the flux of N through the sediment was lost as gases, and that 50'L of the N ammonified from organic matter must have been converted to gases by coupled nitrification-denitrification within the sediments. When compared to the total flux of N through the entire estuary, any N loss by denitrification in the sediments of the upper estuary was minor (-1 X) because of the small surface area of sediment to freshwater flow

The significance of freshwaters as key players in the global budget of both carbon dioxide and methane has recently been highlighted. In particular, rivers clearly do not act simply as inert conduits merely piping carbon from catchment to coast, but, on the whole, their metabolic activity transforms a considerable fraction of the carbon that they convey. In addition, nitrogen is cycled, sometimes in tight unison with carbon, with appreciable amounts being ‘denitrified’ between catchment and coast. However, shortfalls in our knowledge about the significance of exchange and interaction between rivers and their catchments, particularly the significance of interactions mediated through hyporheic sediments, are still apparent. From humble beginnings of quantifying the consumption of oxygen by small samples of gravel, to an integrated measurement of reach scale transformations of carbon and nitrogen, our understanding of the cycling of these two macro elements in rivers has improved markedly in the past few decades. However, recent discoveries of novel metabolic pathways in both the nitrogen and carbon cycle across a spectrum of aquatic ecosystems, highlights the need for new directions and a truly multidisciplinary approach to quantifying the flux of carbon and nitrogen through rivers.

The production of N 2 gas via anammox was investigated in sediment slurries at in situ NO 2 − concentrations in the presence and absence of NO 3 − . With single enrichment above 10 μM 14 NO 2 − or 14 NO 3 − and 15 NH 4 + , anammox activity was always linear ( P < 0.05), in agreement with previous findings. In contrast, anammox exhibited a range of activity below 10 μM NO 2 − or NO 3 − , including an elevated response at lower concentrations. With 100 μM NO 3 − , no significant transient accumulation of NO 2 − could be measured, and the starting concentration of NO 2 − could therefore be regulated. With dual enrichment (1 to 20 μM NO 2 − plus 100 μM NO 3 − ), there was a pronounced nonlinear response in anammox activity. Maximal activity occurred between 2 and 5 μM NO 2 − , but the amplitude of this peak varied across the study (November 2003 to June 2004). Anammox accounted for as much as 82% of the NO 2 − added at 1 μM in November 2003 but only for 15% in May 2004 and for 26 and 5% of the NO 2 − added at 5 μM for these two months, respectively. Decreasing the concentration of NO 3 − but holding NO 2 − at 5 μM decreased the significance of anammox as a sink for NO 2 − . The behavior of anammox was explored by use of a simple anammox-denitrification model, and the concept of a biphasic system for anammox in estuarine sediments is proposed. Overall, anammox is likely to be regulated by the availability of NO 3 − and NO 2 − and the relative size or activity of the anammox population.

Until recently, denitrification was thought to be the only significant pathway for N 2 formation and, in turn, the removal of nitrogen in aquatic sediments. The discovery of anaerobic ammonium oxidation in the laboratory suggested that alternative metabolisms might be present in the environment. By using a combination of 15 N-labeled NH 4 + , NO 3 − , and NO 2 − (and 14 N analogues), production of 29 N 2 and 30 N 2 was measured in anaerobic sediment slurries from six sites along the Thames estuary. The production of 29 N 2 in the presence of 15 NH 4 + and either 14 NO 3 − or 14 NO 2 − confirmed the presence of anaerobic ammonium oxidation, with the stoichiometry of the reaction indicating that the oxidation was coupled to the reduction of NO 2 − . Anaerobic ammonium oxidation proceeded at equal rates via either the direct reduction of NO 2 − or indirect reduction, following the initial reduction of NO 3 − . Whether NO 2 − was directly present at 800 μM or it accumulated at 3 to 20 μM (from the reduction of NO 3 − ), the rate of 29 N 2 formation was not affected, which suggested that anaerobic ammonium oxidation was saturated at low concentrations of NO 2 − . We observed a shift in the significance of anaerobic ammonium oxidation to N 2 formation relative to denitrification, from 8% near the head of the estuary to less than 1% at the coast. The relative importance of anaerobic ammonium oxidation was positively correlated ( P < 0.05) with sediment organic content. This report of anaerobic ammonium oxidation in organically enriched estuarine sediments, though in contrast to a recent report on continental shelf sediments, confirms the presence of this novel metabolism in another aquatic sediment system.